From elements to modules: regulatory evolution in Ascomycota fungi
Introduction
The incredible diversity of living creatures defies their similarity in protein sequence and gene content. King and Wilson [1] first proposed that organismal diversity is likely driven by regulatory differences controlling when, where, and how genetic material is expressed. Nearly 35 years later, although examples of regulatory divergence are known in a wide range of species [2] including bacteria [3], fungi [4], flies [5], and mammals [6], the mechanisms through which regulatory systems evolve are still poorly understood. In recent years, comparative genomics approaches have allowed us to identify the functional components of genomes and to trace evolutionary events at different time scales [7, 8]. These approaches are also being used to infer the evolution of gene-expression regulation through two general approaches: characterization of cis-regulatory elements in orthologous promoter sequences, and comparative analysis of mRNA profiles across organisms. While studies relying on sequence data are more prevalent, functional studies of comparative gene regulation are now starting to shed light on how genome evolution is linked to functional changes.
Among eukaryotes, the Ascomycota fungi (Figure 1a) are particularly suitable for studies of eukaryotic regulatory evolution. More than 100 genome sequences exist for individual strains within Saccharomyces species and across fungi spanning hundreds of millions of years of evolution. They include model organisms (S. cerevisiae and S. pombe) and important human and agricultural pathogens (e.g. C. albicans, Aspergilli, and F. graminarium). Furthermore, sequenced genomes include species that diverged before and after a whole genome duplication (WGD, Figure 1a), which occurred ∼150 million years ago (mya) [9, 10]. This provides a unique opportunity to explore the effect of gene duplication on regulatory divergence. Finally, the relatively small (ca. 9–100 Mb) genomes are computationally tractable, but still display many of the hallmarks of eukaryotic gene regulation.
In this review, we focus on recent advances made in understanding the evolution of gene regulation in Ascomycota, from micro-evolutionary scales (<5 million years and typically within species) to macro-evolutionary time frames over tens of millions of years involving extensive speciation. (It is estimated that S. cerevisiae can undergo ∼2900 generations per year [11].) We examine conservation and divergence from two different perspectives: the regulation of mRNA expression at the level of single genes, and the coordinated expression of genes in regulons or ‘modules’ (i.e. sets of coregulated target genes) within a network. As we show, flexibility and apparent redundancy in gene copies, functional elements and molecular interactions may play a major role in driving the emergence of regulatory divergence, while conserving the functional backbone of transcriptional responses.
Section snippets
Functional and mechanistic corollaries of expression conservation and divergence
Available compendia of genome-wide mRNA profiles have allowed direct comparison of orthologous mRNA expression patterns across species. Large datasets exist for model Ascomycota (S. cerevisiae, S. pombe, and C. albicans), and smaller datasets are available for other fungi in the phylum (e.g. other sensu stricto Saccharomyces [12] C. glabrata [13], K. lactis [14], and some Euascomycota [15, 16]) as well as different strains within S. cerevisiae [12, 17, 18, 19, 20]. Together, these afford a
Gene duplication facilitates regulatory neo-functionalization
Gene duplication may provide a unique opportunity for ED of at least one of the two paralogs [29, 30, 31•]. In a comprehensive study of S. cerevisiae paralogs whose origins range to the last common ancestor with S. pombe (Figure 1a, root) we found surprisingly little divergence of the molecular function of paralogs, but substantial (∼70%) divergence in gene regulation, as reflected in the cis-regulatory elements, the transcription factors (TFs) bound to the genes’ promoters, and the gene
Flexibility in regulatory mechanisms can drive expression divergence
Genetic changes in both cis and trans elements can contribute to ED (Figure 1b). A genetic change can affect expression in cis, either directly by altering regulatory sequences controlling gene expression, or indirectly by modifying the activity of the gene's product and consequently affecting expression through feedback [35]. Polymorphisms in cis appear to contribute most to ED in phylogenetically close species, independent of environmental factors [22••]. Alternatively, a polymorphism distant
Expression divergence in transcriptional regulatory networks
It is challenging to reconcile the substantial evolutionary diversity in the expression of individual genes with the functional organization of regulatory networks. In particular, it is well established that transcriptional modules (regulons of coregulated genes) play a central role in regulatory networks [43, 44, 45]. Various modules are conserved across organisms from E. coli to humans [46, 47], including fungi [21]. However, if the regulation of individual genes is highly evolvable, how are
Conservation of regulatory modules over long evolutionary timeframes
Many regulatory modules are conserved across Ascomycota, often associated with conserved cis-regulatory elements and TFs (Figure 2a). Conserved modules can be identified by a statistically significant overlap in orthologous genes between modules of genes with correlated expression within each species [21, 48]. Alternatively, we can identify conserved regulation in gene modules [4] by comparing cis-regulatory elements enriched in the promoters of sets of orthologous coregulated genes.
Reshaping modules by gain and loss of gene targets
That orthologous regulatory modules can be detected over long time frames does not preclude substantial regulatory evolution. First, coexpression of genes in a module can collectively evolve simply by altering TF activation in response to different environmental cues and upstream signals. Second, cis-regulatory changes can drive gain and loss of targets to affect module composition, as well as regulatory patterns. Although the underlying mechanism is the same, the effects of target gain and
The role of redundancy in mediating regulatory rewiring of conserved modules
The formation of ‘seemingly redundant’ regulatory mechanisms may facilitate the dramatic rewiring of regulatory mechanisms while maintaining gene coregulation. In several cases, wholesale rewiring is observed between species diverged 200–300 mya, and appears to have been preceded by a period of redundant regulation on the order of 100–150 mya.
One prominent mode of redundancy is the formation of a module under the control of multiple regulatory systems, through distinct cis-regulatory sites (
Future prospects
While great advances have been made in the phenomenology and mechanistic understanding of the evolution of gene regulation, the relative roles of neutral drift and selective forces in promoting divergence remain largely unknown. For individual genes, purifying selection can be effectively invoked for the conservation of sites in closely related species, and for the low-ED of genes involved in growth processes. However, it is unclear how much of the increased divergence of high-ED genes is due
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
The authors thank Sigrid Hart for graphics included in the figures. DJW was supported by an NLM training grant 5T15LM007359. DAT was supported by a Human Frontiers Science Program Research Grant. APG was supported by an NSF CAREER award (#0447887) and NIGMS R01GM083989-01. AR was supported by HHMI, by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, by an NIH Pioneer Award and by the Sloan Foundation.
References (67)
- et al.
Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes
Gene
(2006) - et al.
Rewiring of the yeast transcriptional network through the evolution of motif usage
Science
(2005) - et al.
A transcription factor cascade involving Fep1 and the CCAAT-binding factor Php4 regulates gene expression in response to iron deficiency in the fission yeast Schizosaccharomyces pombe
Eukaryot Cell
(2006) - et al.
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
PLoS Genet
(2008) - et al.
Evolution at two levels in humans and chimpanzees
Science
(1975) - et al.
Co-evolution of transcriptional and post-translational cell-cycle regulation
Nature
(2006) - et al.
The evolution of genetic regulatory systems in bacteria
Nat Rev Genet
(2004) - et al.
Conservation and evolution of cis-regulatory systems in ascomycete fungi
PLoS Biol
(2004) - et al.
Emerging principles of regulatory evolution
Proc Natl Acad Sci U S A
(2007) - et al.
Evolution of primate gene expression
Nat Rev Genet
(2006)
Sequencing and comparison of yeast species to identify genes and regulatory elements
Nature
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
Science
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
Nature
Molecular evidence for an ancient duplication of the entire yeast genome
Nature
Evidence for domesticated and wild populations of Saccharomyces cerevisiae
A genetic signature of interspecies variations in gene expression
Nat Genet
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Genome Biol
Transcriptomic analysis of extensive changes in metabolic regulation in Kluyveromyces lactis strains
Eukaryot Cell
A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species
Proc Natl Acad Sci U S A
Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons
Eukaryot Cell
Genetic dissection of transcriptional regulation in budding yeast
Science
Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates
PLoS Genet
Genetic properties influencing the evolvability of gene expression
Science
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast
Proc Natl Acad Sci U S A
A yeast hybrid provides insight into the evolution of gene expression regulation
Science
On the relation between promoter divergence and gene expression evolution
Mol Syst Biol
Control of sochasticity in eukaryotic gene expression
Science
Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors
Genome Res
Two strategies for gene regulation by promoter nucleosomes
Genome Res
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
Nat Genet
Unstable tandem repeats in promoters confer transcriptional evolvability
Science
Duplicate genes increase gene expression diversity within and between species
Nat Genet
Functional analysis of gene duplications in Saccharomyces cerevisiae
Genetics
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These authors contributed equally to this work.